Amino Acids• Colorless, crystalline, water soluble

substances• Distinguishing features are a -COOH group

and a -NH3 group attached to the same carbon

• R group gives individuality• R group varies from a simple H to a complex

phenyl ring• Classification reflects structural feature or

property of R groups

Non-Polar Polar but Uncharged Polar charged (+)

glycinealaninevalineleucineisoleucinemethionineprolinephenylalaninetryptophan

serinethreonineasparagineglutaminetyrosinecysteine

lysineargininehistidine

Polar charged (-)

aspartic acidglutamic acid

Classification

Charges on Amino Acids

COOHC-

H

R

Zwitterion(Rhymes with “bitter ion”)

pKa = 2

pKa = 9.5

N:

H H

R C-

COO

N

H

+H

H

H

See Tutorial “Ionization” on

Web

See Tutorial “Ionization” on

Web

GLYCINE

H C -

NH3

COO -

HCH3

Alanine

CH2OH

Serine

Stereochemistry

COO-

CH3N H

R

L-amino acid*

Amine group left

Chiral center

Take Home: All amino acids that occur in proteins are of the L configuration

Carboxyl group up

When R=H, no chiral center

Chirality or “handedness”

4 Different Substituents

L L D

COO

H3N HC+

R

COO

H C

R

NH3

+

L D

Mirror Image

Mirror ImageReproduced

Mirror ImageNot Reproduced

Chiral Center No Chiral Center

CHARGE ON AMINO ACIDS DEPENDS ON

pH OF SOLUTION

COOHCCH3

H3N H+ COO

CCH3

H3N H+ COO

CCH3

H2N H

+ 1 0 -1

Conjugate Conjugate

pH 1-2 pH 3-8 pH 9-12

Glycine Gly G 2.34 9.6Alanine Ala A 2.34 9.69Valine Val V 2.32 9.62Leucine Leu L 2.36 9.6Isoleucine Ile I 2.36 9.6Serine Ser S 2.21 9.15Threonine Thr T 2.63 10.43Methionine Met M 2.28 9.21Phenylalanine Phe F 1.83 9.13Tryptophan Trp W 2.83 9.39Asparagine Asn N 2.02 8.8Glutamine Gln Q 2.17 9.13Proline Pro P 1.99 10.6Cysteine Cys C 1.71 10.78 8.33Histidine His H 1.82 9.17 6.0Aspartic acid Asp D 2.09 9.82 3.86Glutamic acid Glu E 2.19 9.67 4.25Tyrosine Tyr Y 2.2 9.11 10.07Lysine Lys L 2.18 8.95 10.79Arginine Arg R 2.17 9.04 12.48

2.20 9.52

Amino Acid Abbreviations pK1 pK2 pK3

Table 1: Approximate pK values for Ionizable Groups in Amino Acids

Group Amino Acid Approx. pK

-carboxyl All 2.0-amino All 9.5-carboxyl Aspartic acid 4.0-carboxyl Glutamic acid 4.0imidazole N Histidine 6.0thiol SH Cysteine 8.5phenolic OH Tyrosine 10.5-amino Lysine 10.5guanidinium N Arginine 12.5

estimate charges on the molecule for a given pH.

Know these values

Biochemical Strategies p. 32

Titration Curve for an Amino Acid

pK1=2pK2=9.5

pH

0 1.0 1.5 2.00.5

2.0

9.5 -COOH

Equivalents OH-

Glycine

-COOH

-COO-

H3N-+

H2N-

H3N-+

To draw a titrationcurve, (1) determinenumber of dissociable groups, (2) place pK values in centerof range (3) draw curve.

COOHH-N-C-H

H

H

H

+

pH

pK3 = 9.5

pK2 = 4.0pK1 = 2.0

0 1.0 2.0 3.0

2

4

8

Equivalents of OH-See Strategies p. 33

-HCOOHC

CH2

CH2

COOH

H3N-+

-HCOO-

C

CH2

CH2

COOH

H3N-+

-HCOO-

C

CH2

CH2

COOH

H3N-+

-HCOO-

C

CH2

CH2

COO-

H3N-+

-HCOO-

C

CH2

CH2

COO-

H3N-+

-HCOO-

C

CH2

CH2

COO-

H2N-

-HCOOHC

CH2

CH2

COOH

H3N-+

L-Glutamate

Isoelectric Points

1. pH at neutral charge (note the word “pH” in the definition)

(pI) of Amino Acids

2. pI = pK1 + pK2

2

pK1

pK2

Simple Amino Acid

pI

pK1 + pK2

2

pI for an Amino Acid with a Charged R Group

COOHC

CH2

COOH

H3N H+

1 pK = 2

2 pK = 4 3

pK = 9.5

2

4

6

8

pH

pK1pK2pK3

?

?

0 -1 -2

+1

Rule: Always use the 2 pKs that border the “0” charged species

COOC-HH3N-

+

CH2

CH2

CH2

CH2

H3N+

pH 7 = +1

H

pH 1= +2

2

4

6

8

10

12

+2 +1 0 -1

pI = about 10

pK1= 2

pK2= 9.5

pK3= 10.5

pI = pK2 + pK3

2=

9.5 + 10.5

2= 10

Lysine is a basic amino acid

Isoelectric Point of Lysine

Table 2: Classification of Amino Acids based on R group Features

Aromatic Sulfur Basic Amide

Phenylalanine Cysteine Lysine AsparagineTyrosine Cystine Histidine GlutamineTryptophan Methionine Arginine

Hydroxy Hydrophobic Acidic

Serine Leucine Aspartic acidThreonine Isoleucine Glutamic acid

Valine

See Strategies, p 35See Strategies, p 35

Non-polar

Polar non-charged

Charged acidic

Charged basic

CH2NN

CH2

HH

Imidazole

+

PhenylL-HistidineL-Phenylalanine

CH2

CH3H3CIsopropyl

L-Valine

Thioether

L-Methionine

SCH3

CH2

CH2

CH2

CH2

CH2

NHH2N=C

NH2

+

GuanidinoL-Arginine

CH2OHL-Serine

CH2SH

L-Cysteine

CH2CH2COO-

L-Glutamate

HGlycine

CH3

L-AlanineCCOO-

H3N H+

NCOO-

H

L-ProlineSecondary amine

L-Tryptophan

Indole ring

NH

CH2

CH2

CH2

CH2

CH2

H3N+

L-Lysine

L-Threonine

H-C-OH

CH3

*

CCOO-

H3N H+

See Tutorial on Amino Acid Structures on Web

See Tutorial on Amino Acid Structures on Web

A = AlanineC = CysteineD = Aspartic acid

E = Glutamic acidF = PhenylalanineG = Glycine

H = HistidineI = Isoleucine

K= LysineL = LeucineM = Methionine

P = ProlineQ = Glutamine

N = Asparagine

R = ArginineS = Serine

T = ThreonineV = ValineW = Tryptophan

Y = Tyrosine